*warning I go completely off on a tangent in this post*
If you still like old school side scroller action. Its hard to beat a GBadv/DS. (ignoring emulators on the PC)
Some games/playstles simply don't translate well to 3D. Castlevania symphony of the night sold hand and fist over any 3d incarnation of the series. While the latest wii edition of Metroid is pretty darn good super metroid I still overall had more fun with. Side scroller beatemups/shooters like golden axe, streets of rage, contra, metal slug, bionic commando. Puzzle/adventure platformers. 2D 1vs1 fighters (though I feel soul calibur did a great job mixing the 2D "feel" in a 3d play area) and the list goes on.
A lot of these genres don't quite translate the original feel well to 3D. That's not always a bad thing, but in many cases on a personal level I still feel the 3D counterparts haven't caught up yet in overall fun.
I feel super mario world 3 from a fun and gameplay point of view still is superior to every 3D version that came out of the mario series including the wii version.
2D sidescroller games are still released on the nintendo hand helds. And for me (and it seems many in general) the real fuel behind a console is the experiences it can provide you and that is usually dominated by what games it makes available to you. Sometimes I get lucky and something like Bionic Commando Rearmed comes along. But that's pretty rare.
At some point, a user interface will be refined where it becomes cheap but very very 3d friendly. Along the lines of a head tracking system plus a wiimote control scheme, perhaps even plus something with your legs.
On a 2d you can pretty much "see" everything so leaving the "camera control" to the game isn't an issue. In 3d without head tracking, looking around you is somewhat of a chore, it shouldn't be.
In 2d there are only 360degrees of angles, in 3D there is 360degrees squared. Thus a pointer type device such a mouse/track/wiimote is crucial for accuracy of intentions.
Lastly movement, once again you go from 360degrees to 360degree squared in theory...but since most of the time you're on the ground it becomes limited to just 360degrees.
With two analog sticks you can only control two sets of 360. Which usually load movement to one stick and view+interaction on the other.
In general this feels sluggish and clumsy compared to the snap action of 2d because you simply lack the finesse of input needed to really make 3D respond to your desires.
If you have good head-tracking you get 360^2 view angle input intuitively tied to your natural movement.
If you have a pointer device you get 360^2 of range of motion for interacting with things in your view.
This leaves at least one analog stick for movement.
At that point I'll guess that most 3D titles should feel much much more intuitive and responsive and the interface will really be more on par with the environment. The tech is there for this of course, but the price and support really isn't. Someday though.
Until then there is a bit of fluidity that 2d games have which 3d ones don't in various cases.